rs10003892

Variant names:

• chr4-6205057-G-A
• rs10003892
• ENST00000507424.1:n.2529G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507424.1(ENSG00000251408):​n.2529G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,092 control chromosomes in the GnomAD database, including 21,149 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.52 (21136 hom., cov: 31)
  • Exomes 𝑓: 0.56 (13 hom.)
• Consequence: ENSG00000251408 ENST00000507424.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 1 publications found

Genes affected

ENSG00000251408 (HGNC:):

JAKMIP1-DT (HGNC:27728): (JAKMIP1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507424.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAKMIP1-DT	NR_037863.1		n.207+4118G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251408	ENST00000507424.1	TSL:2	n.2529G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000290803	ENST00000508601.2	TSL:2	n.207+4118G>A		intron	N/A
	ENSG00000290803	ENST00000776984.1		n.155+5190G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78977 AN: 151880 Hom.: 21133 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.564 AC: 53 AN: 94 Hom.: 13 Cov.: 0 AF XY: 0.569 AC XY: 41 AN XY: 72

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.875 AC: 7 AN: 8

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.561 AC: 37 AN: 66

Other (OTH) AF: 0.375 AC: 3 AN: 8

GnomAD4 genome AF: 0.520 AC: 79015 AN: 151998 Hom.: 21136 Cov.: 31 AF XY: 0.517 AC XY: 38417 AN XY: 74282

African (AFR) AF: 0.381 AC: 15792 AN: 41450

American (AMR) AF: 0.488 AC: 7450 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1932 AN: 3470

East Asian (EAS) AF: 0.595 AC: 3064 AN: 5152

South Asian (SAS) AF: 0.508 AC: 2448 AN: 4822

European-Finnish (FIN) AF: 0.544 AC: 5745 AN: 10566

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40795 AN: 67958

Other (OTH) AF: 0.540 AC: 1139 AN: 2110

Alfa AF: 0.571 Hom.: 10416

Bravo AF: 0.509

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10003892;

hg19: chr4-6206784;